The Africa Inland Mission was first founded in Machakos, Kenya in 1885 and later moved to what is now the DRC in 1912. From there the AIM started working in the southern Sudan in 1949. According to the Sudan Missionary Regulations of 1905, different missions should work in separate and clearly defined areas, with the exception of the eastern districts which were declared an "open space" where any mission could work. In good understanding with the Anglican Church in southern Sudan the AIM agreed to take up responsibility for the whole of Eastern Equatoria, releasing the CMS to concentrate on their rapidly growing churches on the west bank of the Nile. The new mission was staffed by American as well as Congolese missionaries. Medical work played a significant role. A clinic which began as a small health centre has now been developed into a big hospital. In 1955 all foreign missionaries had to leave Southern Sudan and the development of national leadership became an urgent priority, even though the mission was still young. The first Sudanese AIM pastor was ordained in 1956. In 1972 the church became fully autonomous, with a membership of about 1,000. Under its indigenous Sudanese leaders the church began to grow steadily as of 1973.

The African Inland Church Sudan is Trinitarian, confesses the divinity of Christ and accepts the scriptures of the Old and New Testament as the absolute and final authority in all matters of faith and conduct. The highest governing body of the AIC Sudan is the general assembly, under which exist regional, district and local church councils. A central church council, elected by the general assembly, is responsible for implementing the decisions of the assembly and for the overall administration of the church. Gospel campaign actions including church planting, discipleship training, seminars and conferences are core activities. The pastors of the church are trained at various evangelical institutions in Sudan and abroad.

Currently the church is running service programmes focusing on basic education and primary health care. Other programmes include skill training for displaced persons, especially women, and sanitation and housing development in camps around Khartoum. The church is also involved in relief work in the Darfur area. In the new peace era the churches in Sudan are required to give priority to counselling and reconciliation programmes for persons returning after the war as well as for those who remained at home throughout the war.